Millennial clonal persistence and transposable element-biased somatic mutations in an herbaceous plant (Typha latifolia)

cloneⱼzg22This script we used for jzg population analysis with 2022 refenrence data 01 build the reference genomeScripts we used for build the reference are in 01ᵣef. 02 check clone Scripts we used for checking clone and call variants are in 02checkclone. 03 estimate population ageScripts we uesd for estimating the T. latifolia clonal population age in 03ₑstimateₚopulationₐge. 04 clonal development routesScripts we uesd for build the clonal phylogenetic tree, and map the tree to the geographic locations in 04clonaldevelopmentᵣoutes. 05 characteristic of somatic mutationsScripts we uesd for checking position, direction of somatic mutations. meanwhile, check the non-synonymous mutation site during the development and the vaf of somatic mutations in 05ₚositiondirectionᵥaf. 06 data Files that we used as material or the file lists we used for analysis are in data.